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Posted by on 8:06 pm in Welcome | Comments Off on

Computational Science is widely recognized as a critical means to solving many of today’s most challenging problems.  The analysis and knowledge gained from working with the incredible data explosion produced by massive experiments, observations and computer generated models is leading to solutions at an unimagined pace. Data-Intensive discovery (the fourth paradigm of scientific research), and Multi Scale Interdisciplinary  approaches are becoming more prevalent in the way that Science and Engineering is generating...

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“Connections, Connections: Student Research in Social Systems @ UM” 9/21

Posted by on 10:25 am in Engagement, Events - Past, Lectures & Seminars - Archived, News - Archived | Comments Off on “Connections, Connections: Student Research in Social Systems @ UM” 9/21

“Connections, Connections: Student Research in Social Systems @ UM” 9/21

A Flash Talks and Networking Symposium Friday, September 21, 2018 | 4:00-6:00 PM Ungar Building, Room 230C-D | RSVP Now It is a pleasure to invite you to Connections, Connections: Student Research in Social Systems @ UM, organized by the Center for Computational Science. Social informatics includes modeling big behavioral data to understand human and non-human social interaction. Students working in psychology, education, geography, public health, or architecture; students studying sociality in model organisms; or students working on method development through computer science, mathematics, physics and engineering, may fall under the Social Systems Informatics umbrella. This event offers an opportunity for post-doc, graduate (and advanced undergraduate) students across campuses to connect, share their research, and network with each other and with invited faculty. Agenda Ice breaker Five-minute student flash talks (6x) Networking   Guide for Presenters We are calling all students who would like to present a flash talk. Presentations are maximum 5 minutes, followed by up to 5 minutes of questions. You may prepare a slide deck with a maximum of 5 slides. If interested in attending or presenting, please register. Important dates for presenters: 9/14 Deadline to Register to be a Presenter 9/19 Presentation Slides Submission Deadline 9/21 Date of Presentation For any questions regarding the event, please contact us at ccsengagement@miami.edu   We look forward to seeing you at Connections, Connections: Student Research in Social Systems @ UM.  This event is free and open to UM Faculty, Staff, and Students. Location The Leonard and Jayne Abess Center for Ecosystem Science and Policy Arthur A. Ungar Building, Room 230C-D 1365 Memorial Drive, Coral Gables, FL 33146          ...

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CCS Software Engineering Drone Maps Oldest Surviving Synagogue in Curacao

Posted by on 9:56 am in News | Comments Off on CCS Software Engineering Drone Maps Oldest Surviving Synagogue in Curacao

CCS Software Engineering Drone Maps Oldest Surviving Synagogue in Curacao

The shifting sands on the floor inside the Western Hemisphere’s oldest continuously operating synagogue Mikvé Israel-Emanuel in Willemstad, Curaçao posed some unique challenges. Covering the floors of the sanctuary and the mezzanine, the sand parted with every footfall, making it harder for eight University of Miami School of Architecture students to document every cornice and crevice of the synagogue, built nearly 300 years ago by Dutch Jews whose descendants fled the Spanish Inquisition. “Sometimes it’s a bit overwhelming,” said Olivia Kramer, a fifth-year student (on the left, below) from Minnesota who sketched much of the floor plan of the triple-vaulted building that opened its mahogany doors in 1732. “We’re on hands and knees measuring every inch. We’re double-checking every dimension. I don’t think I’ve ever been so dirty. We leave the synagogue soaked in sweat and with sand in our shoes.’’ Yet Kramer and the other architecture students (L-R Olivia, Joshua Kleinberg, Amanda Arrizabalaga, Xiangyu "Jack" Shao, Daniella Huen, and Hector Valdivia Arrieta)—who spent the first week of the fall semester on this Dutch Caribbean island just north of Venezuela—had no complaints. They may not have known exactly what they were getting into when they signed up for Professor Jorge L. Hernández’s elective design studio in historic preservation, but the arduous process of creating the most comprehensive and accurate architectural drawings of the oldest surviving synagogue in the Americas was an exhilarating learning experience with innumerable rewards. Among them was laying the foundation for their school’s proposed collaboration with UM’s Institute for Advanced Study of the Americas, Miller Center for Contemporary Judaic Studies, Center for Computational Science, and College of Arts and Sciences, to create an architectural and historical record of all the Caribbean’s Jewish synagogues and temples. [Making the trip from CCS was Software Engineering Director Chris Mader (at right) and Associate Scientist Amin Sarafraz (at left) who drone mapped the interior and exterior of the Synagogue.] “We want to document [the synagogues] one by one, and this is a perfect pilot project and a perfect place to start,” said Haim Shaked, director of the Miller Center. “It is a unique building with a unique history. It was modeled after the main synagogue in Amsterdam, which welcomed Jews expelled from Spain and Portugal, and you feel the history when you walk in." Added UM’s first lady, Felicia Marie Knaul (whose idea it was for UM to survey the Caribbean’s synagogues): “The Nazis destroyed many of the synagogues in Europe, and we don’t want time or neglect to destroy the places in our hemisphere where Jews found refuge and prospered for centuries.” Divided into a floor plan team and a longitudinal sections team, the students spent six long, hot days measuring and sketching the un-airconditioned space imbued with serenity and history and bathed in cobalt light. The color filtered through dozens of blue stained-glass windows that, depending on the time of day, splashed the sills, the white walls, the mahogany benches, and the mysterious, ubiquitous sand with its heavenly blue hue. “The simplicity is luminous,” said fourth-year student Hector Valdivia Arrieta, a recent transfer from Peru who would leave Curaçao enamored with his first taste of preservation work. “When the work is tedious you can rest your mind in a place filled with inspiration. Just lie down on the sand floor and...

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Notification: /scratch and /projects may be intermittently unavailable . . .

Posted by on 9:23 am in News - Archived | Comments Off on Notification: /scratch and /projects may be intermittently unavailable . . .

Notification:  /scratch and /projects may be intermittently unavailable . . .

Attention All Pegasus Users:  /scratch and /projects may be intermittently unavailable until further notice due to problems with the storage controllers. We are aware of the situation and are working on resolving the issues. We will send updates as more information is known. As always, if you have any questions or problems, please contact us by sending email to: hpc@ccs.miami.edu....

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“Fundamentals of Java Programming” by Mitsu Ogihara now available

Posted by on 10:26 am in News | Comments Off on “Fundamentals of Java Programming” by Mitsu Ogihara now available

“Fundamentals of Java Programming” by Mitsu Ogihara now available

 Fundamentals of Java Programming by CCS Big Data Analytics & Data Mining Program Director Mitsunori Ogihara is now available in hardback. Making extensive use of examples, Fundamentals of Java Programming teaches the fundamental skills for getting started in a command-line environment. Meant to be used for a one-semester course to build solid foundations in Java, the textbook eschews second-semester content to concentrate on over 180 code examples and 250 exercises. Key object classes (String, Scanner, PrintStream, Arrays, and File) are included to get started. The programs are explained with almost line-by-line descriptions, also with chapter-by-chapter coding exercises. Teaching resources include solutions to the exercises, as well as digital lecture slides.   About the Author Mitsu Ogihara is a professor of Computer Science at the University of Miami, Coral Gables, FL. Prior to joining the UM, he was a professor of Computer Science at the University of Rochester, Rochester, NY. He is presently an editor of Theory of Computing Systems (Springer), International Journal of Foundations of Computer Science (World Scientific Press), and Open Computer Science Journal (De Gruyter). He has published three books: A Complexity Theory Companion (Springer), Music Data Mining (CRC Press), and Fukuzatsusa no KaisoÌ in Japanese. He has published more than 190 research...

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Join us for the 2018-2019 CCS Fellows’ Launch Symposium 8/16/18

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Join us for the 2018-2019 CCS Fellows’ Launch Symposium 8/16/18

The vision of the Center for Computational Science’s “CCS Fellows Program” is to inspire a new generation of leaders in computational science to cross the traditional boundaries between disciplines, by equipping them with new cross-disciplinary skills and experience. The Program does this by offering mentorship outside the students’ area of expertise. “CCS Fellow” is a prestigious designation awarded to two undergraduate students and two graduate students per year. Join us on Thursday, August 16, 2018, 3:00-5:00 PM, at Gables One Tower, for the 2018-2019 CCS Fellows' project launch presentations. This event is free and open to interested UM Faculty/Staff/Students.  Refreshments will be served. Please RSVP Location Gables One Tower, Training Room 639, 1320 S Dixie Hwy, Coral Gables, FL 33146  |  Map | Directions   Meet the CCS Fellows:   Yeo Jin "Amy" Ahn Project  Automating and Accelerating the Autism Diagnostic Process Mentors Mitsunori Ogihara, PhD | Dept. of Computer Science and CCS Daniel S. Messinger, PhD  |  Professor of Psychology Amy is a PhD student in Psychology. She graduated with honors from Cornell University with a B.S. in Human Development and a concentration in Social and Personality Development. She joined the Early Play and Development Lab in fall of 2017. She is interested in infants' and young children's social interaction and how it relates to typical and atypical social and emotional development. She aims to better understand children's social behaviors by implementing objective measurement. Steven Anderson Project  Virtual Reality Simulations of Dyadic Medical Interactions Mentors Mitsunori Ogihara, PhD | Dept. of Computer Science and CCS Elizabeth Reynolds Losin, PhD  |  Department of Psychology - Health Division Steven is a PhD student working under the supervision of Dr. Elizabeth Losin in the Cognitive and Behavioral Neuroscience Division in the Department of Psychology. He received his Bachelor of Liberal Arts in Psychology from Harvard University Extension School. Prior to joining the Social and Cultural Neuroscience Laboratory at the University of Miami, Steven worked on developing behavioral health interventions for patients with chronic medical conditions at a healthcare technology company. His doctoral research centers on identifying sociocultural and contextual influences on pain perception in the self and others, with an applied focus on medical settings and the doctor-patient relationship. His research utilizes behavioral, neuroimaging, psychophysiological, and computational methods. Jin Yop "Stephano" Chang Project  Development of Closed-Loop Neuromodulation of Gait and Balance Control After Spinal Cord Injury Mentors Brian R. Noga, PhD and James D. Guest, MD PhD FACS FRCS (C) | The Miami Project to Cure Paralysis Odelia Schwartz, PhD  |  Department of Computer Science Stephano is a Neurosurgery resident pursuing his PhD in Neuroscience with Dr. Brian Noga and Dr. James Guest at the University of Miami Project to Cure Paralysis, combining his clinical background with his scientific interest in neuromodulation for spinal cord injury. During the CCS Fellows program, he hopes to apply a computational approach to optimize the application of neurostimulation technologies to restore function after injury. Samantha Mitsven Project  Objective Measurement of Language Development: An Investigation of Preschoolers' Networked Social Interactions Mentors TBA Daniel S. Messinger, PhD  |  Professor of Psychology Samantha received her B.A. in Psychology from San Diego State University in 2013 and worked as a Research Assistant and Lab Manager in cognitive and neuroimaging labs at UC Davis and Stanford University following graduation. She is currently a second year PhD student in Developmental Psychology working...

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Ben Kirtman Named American Meterological Society Fellow

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Ben Kirtman Named American Meterological Society Fellow

CCS Director of Climate & Environmental Hazards program and RSMAS Professor Ben Kirtman is named 2019 fellow of the American Meteorological Society (AMS) for his outstanding contributions to weather, water, and climate. He will be recognized during the AMS Annual Meeting on January 9-11, 2019, in Phoenix Arizona. Kirtman, who has been at the UM Rosenstiel School for over 10 years, is a professor of Atmospheric Sciences and director of the Cooperative Institute for Marine and Atmospheric Studies (CIMAS).   “This long overdue recognition for Ben reflects his status in our professional society and brings prestige to him, our School and our University,” said Dean of the UM Rosenstiel School Roni Avissar. Kirtman is a climate modeler who uses complex Earth system models to investigate the predictability of the climate system on time scales from days to decades and to study the influence of tropical variability on mid-latitude predictability. His research is wide-ranging and designed to understand and quantify the limits of climate predictability from days to decades, including understanding how the climate will change in response to changes in man-made and natural forcing. He was one of the first to develop an El Niño/La Niña prediction system using sophisticated climate models and currently leads a team of government laboratory researchers, academicians, and operational climate forecasters in developing the North American Multi-Model Ensemble (NMME) prediction system. This new prediction system has been issuing forecasts in real-time since August 2011, and was instrumental in predicting continuing La Niña conditions in the tropical Pacific and the associated impact on climate around the globe. The NMME became an official NOAA operational system in May 2016. The author of more than 120 peer-reviewed publications, Kirtman was also a coordinating lead author of the Intergovernmental Panel on Climate Change’s (IPCC) 5th Assessment Report and is a member of several national and international scientific panels and working groups. Kirtman joins UM Rosenstiel School professors and current AMS fellows Brian Soden, Amy Clement, Lynn “Nick” Shay, Roni Avissar, and Bruce Albrecht. Founded in 1919, the American Meteorological Society (AMS) is the nation’s premier scientific and professional organization promoting and disseminating information about the atmospheric, oceanic, and hydrologic sciences. Our more than 13,000 members include researchers, educators, students, enthusiasts, broadcasters and other professionals in weather, water, and climate.   SOURCE:  UM News & Events Rosenstiel School Professor Named American Meterological Society...

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UM CCS Accelerates Life Sciences: A DDN Storage Success Story

Posted by on 10:09 am in News | Comments Off on UM CCS Accelerates Life Sciences: A DDN Storage Success Story

UM CCS Accelerates Life Sciences: A DDN Storage Success Story

ACCELERATE: LIFE SCIENCES A featured DDN Success Story, CCS Advanced Computing correlates viruses with gastrointestinal cancers for the cancer genome atlas 400% faster!     CHALLENGES • Diverse, interdisciplinary research projects required massive compute and storage power as well as integrated data lifecycle movement and management • Highly demanding I/O and heavy interactivity requirements from next-gen sequencing intensifi ed data generation, analysis and management • Powerful, flexible file system was required to handle large parallel jobs and smaller, shorter serial jobs • Data surges during analysis created “data-in-flight” challenges   SOLUTION An end-to-end, high performance DDN GRIDScaler® solution featuring a GS12K™ scale-out appliance with an embedded IBM® GPFS™ parallel file system   RESULTS • Links between certain viruses and gastrointestinal cancers discovered with computation not possible before • With DDN’s high performance I/O, CCS has reduced genomics compute and analysis time from 72 to 17 hours   BUSINESS BENEFITS • The ability to meet varied research workflow demands enables CCS to accelerate data analysis and speed scientific discoveries • Best-in-class performance for genomics assembly, alignment and mapping has proven invaluable in supporting major medical research into Alzheimer’s, Parkinson’s and gastrointestinal cancers • High performance storage and transparent data movement lets CCS scale storage without adding complexity   The University of Miami Center for Computational Science (CCS) maintains one of the largest centralized academic cyber infrastructures in the country, which is integral to addressing major scientific challenges, and solving many of today’s most challenging problems. Working with CCS, more than 2,000 researchers, faculty, staff, and students across multiple disciplines collaborate on diverse and interdisciplinary projects requiring Advanced Computing resources. CCS provides hardware, software development, and analytics expertise to support a variety of research areas, including: Genomics Computational Biology Marine Ecosystems Ocean Modeling Climate and Meteorology Computational Economics Computational fluid dynamics, and Social Systems Informatics. According to Dr. Nicholas Tsinoremas (CCS Center Director and Professor of Medicine, Computer Science, and Health Informatics), CCS was founded on the premise that data drives discovery. Therefore, keeping pace with data growth is of paramount importance. “Data-intensive discovery and multi-scale interdisciplinary approaches are becoming more prevalent in the way that sciences and engineering generate knowledge,” Nick explains. “The speed at which scientific disciplines advance, depends in large part on how effectively researchers collaborate with one another and with experts in the areas of workflow management, data management, data mining, decision support, visualization, and cloud computing.” Another guiding principle is the imperative to manage the entire data lifecycle as seamlessly as possible to streamline research workflow. “We have integrated the Advanced Computing environment with our data capture and analytics environments, so movement is transparent between different research steps,” Nick adds. “This level of interactive processing speeds the delivery of data from sensors and instruments to the desktop of analysts and ultimately, into the hands of science-based decision makers.”   THE CHALLENGE Unlike other advanced computing centers that originated as simulators, CCS has always put a lot of emphasis on data driving scientific results. Approximately 50% of the Center’s users come from UM’s Miller School of Medicine with ongoing projects at the John P. Hussman Institute for Human Genomics (such as research into Alzheimer’s disease), and The Miami Project To Cure Paralysis. The remaining 50% of users cover Marine and Atmospheric Sciences (RSMAS) as well as Engineering, along with...

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A Look Back at Our History: The CCS 10-Year Report (2007-2017)

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A Look Back at Our History: The CCS 10-Year Report (2007-2017)

The University of Miami Center for Computational Science (CCS) proudly celebrates 10 years of projects and collaborations . . . Thank you to all who shared in this journey.  

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Notification: CCS Storage System Maintenance Begins 7/3 at 7 AM

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Notification:  CCS Storage System Maintenance Begins 7/3 at 7 AM

From 7:00 AM to 12:00 AM on Tuesday July 3rd, storage systems for the Pegasus compute cluster, Apollo, and VISX will undergo hardware maintenance. During this maintenance period, Pegasus batch execution and login nodes will be unavailable—as will the gateway (gw.ccs.miami.edu), Apollo, and VISX systems. We apologize for the inconvenience, and thank you for your understanding and cooperation. We will send out an all clear message once the work is done. As always, if you have any questions or problems, please contact us by sending email to: hpc@ccs.miami.edu....

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Post-Conference Report “Big Data in Health” 2018

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Post-Conference Report “Big Data in Health” 2018

The "Big Data in Health" Conference was held at Salerno (Italy) on June 6-8, 2018. The event was organized by Enrico Capobianco (CCS Computational Biology & Bioinformatics program, University of Miami, FL-US) in collaboration with the Universities of Salerno, Perugia, Roma (Cattolica), and was co-sponsored by Roche Pharma Italy. Follow up publications will appear in Frontiers in Medicine and Journal of Clinical Medicine. About 60 people registered and participated to the 5 sessions in the program. The audience was a mix of clinicians, academicians, researchers in industry, health administrative sector-, and other health professionals, thus confirming the spirit of the initiative aimed to propose an integrative multidisciplinary approach to Big Data in Health, particularly from the Electronic Health Records perspective. Advances in Precision Medicine, wellbeing and biological age were proposed, together with studies covering a spectrum of complex diseases (cancer, CVD, kydney, AR, epilepsy). Presentations are available at the links below. Big Data in Health are already exerting a profound impact on biomedicine. Examples include: The centrality of Electronic Health Records (EHR) in public health and epidemiological studies and in scientific publications The foundational role of high-throughput genomics and integrated multiplexed omics to advance experimental biology The depth at which high-resolution imaging is achieving unprecedented accuracy In light of the emerging digital medicine paradigm, the role of digital phenotypes has become crucial to characterize diseases. Comprehensive approaches are now conceived for the analysis of multi-evidenced data, i.e., data generated from multiple sources, such as cells, organs, individual lifestyle and social habits, environment, population dynamics, etc. The other emerging N-of-1 paradigm is inspired by individualization of care and cure. Health across wellbeing and disease stages is leveraging through technology the idea of connectedness, thus converging to a dichotomy already in use at the social level, i.e. ‘connected being’ vs ‘disconnected being’. Through examples of recent and ongoing studies and applications, the main questions addressed at the 2018 Big Data in Health Conference were: Is digitalization being disruptive in health? Are EHR filling the knowledge clinical gaps in support of patients? What are the major bottlenecks and fast tracks for healthy ageing? How Big Data can help doctors stop big killers?   Riepilogo degli interventi  |  2018 Big Data in Health Talks Luigi Pavone - IRCCS Neuromed Pozzilli (IS) "A Machine Learning Approach to Detect Siezures in-Patients with Drug-Resistant Epilepsy by Luigi Pavone" Gennaro Galasso - Università degli Studi di Salerno "Big Biomedical Data and Cardiovascular Disease" Giovanni Veronesi (with Antonella Zambon) - University of Insubria, Varese "Big Data and Precision Prevention Opportunities and Challenges for Biostatisticians" Alessandro Gialluisi, PhD - IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS) "Big Data Approaches for the Estimation of Biological Age: A New Perspective for the Moli-sani Study" Robert Alexander, MD - IBM Italia "Big Data, Big Mistakes, Artificial Intelligence, and The Future" Alberto Sanna - Direttore Centro Technologie Avanzate per la Salute ed il Benessere nei Sistemi Socio-Tecnologici "I Big Data e l’Ingegneria della Consapevolezza La Salute ed il Benessere nei sistemi socio-tecnologici" Marialuisa Sensi - Fondazione IRCCS Istituto Nazionale dei Tumori "Definition of Consensus Melanoma Subtypes with Distinct Phenotypes and Clinical Implications" Roberta Bosotti - Nerviano Medical Sciences s.r.l. "Development of Personalized Medicine in Oncology" Roberto Scalamonga - Roche "Diagnostic Innovation and Personalized Therapeutic Opportunities for Cancer Patients" Federica Cabitsa - Università degli...

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